title: PADI Library 3, Bin 12


title: PADI Library 3, Bin 10

status: Public on May 19 2024

type: SRA

city: Durham

first: Lucia

middle: C.

last: Strader

state: NC

address: 124 Science Drive 3332 French Family Science Center

department: Biology

country: USA

institute: Duke University

library_source: genomic

data_processing:
bwa-mem 0.7.17-r1188 was used to perform alignment of reads to the designed DNA fragment library
samtools v1.10 was used to generate sorted BAM files and extract read counts aligned to each fragment
Supplementary files format and content: CSV files with Fragment Name, AD AA sequence, Designed DNA sequence, Number of Reads
Library strategy: Amplicon

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MATa TF Library x MATalpha Reporter Strain

extract_protocol:
Sorted cells were grown overnight and then pelleted. Genomic DNA was extracted from cell pellets with YeaStar Genomic DNA Kit (Zymo Research).
Sequencing libraries were generated through three PCR reactions. PCR1 amplified a 600bp fragment that contained the tested fragment from the integrated locus. PCR2 amplified the fragment itself and added phasing and Illumina sequencing adapters. PCR3 completed the Illumina sequencing adapters and added indexes to each sample that were specific for each bin and yeast library tested.

treatment_protocol: Overnight cultures were diluted 1:5 in SC with 1 µM beta-estradiol and grown for 4 hours at 30 °C before sorting on the BC Astrios or BD Aria-II

tag: cell line


title: HEK293T_A21

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

library_source: transcriptomic single cell

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to exon regions or intron regions by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted by exon fragments and intron fragments respectively.
Assembly: hg19, mm10
Supplementary files format and content: Tab-separated UMI count matrix (exon based); Files: HEK293T_exon_UMI_count_matrix.txt, HPNE_exon_UMI_count_matrix.txt, U2OS_exon_UMI_count_matrix.txt
Supplementary files format and content: Tab-separated UMI count matrix (intron based); Files: HEK293T_intron_UMI_count_matrix.txt, HPNE_intron_UMI_count_matrix.txt, U2OS_intron_UMI_count_matrix.txt
Supplementary files format and content: Number of reads mapped to different species, Tab-separated table (for mixed species experiment); File: Mixed_species_summary.txt

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Cells are trypsinized and resuspended in PBS. Single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following snapTotal-seq protocol.


title: PADI Library 2, Bin 9

value: MATa TF Library x MATalpha Reporter Strain


title: PADI Library 2, Bin 8


title: PADI Library 3, Bin 7


title: HEK293T_A22


title: PADI Library 2, Bin 7


title: PADI Library 2, Bin 6


title: HEK293T_A19


title: HEK293T_A18


title: PADI Library 2, Bin 5


title: snDNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq DNA library - second reaction)

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
snRNA-seq data were processed as described previously [Yuan and Sims, Scientific Reports, 2016]. The code is available at (https://github.com/simslab/DropSeqPipeline8). Briefly, we aligned the transcriptomic reads (read 2) to the human or mouse genome and transcriptome annotation using STAR v2.7.0d [Dobin et al, Bioinformatics, 2013]. For human data sets other than the mixed species experiment, we used GRCh38/Gencode v24. For the mixed species data set, we used a concatenated genome and annotation comprised of GRCh38/Gencode v32 and GRCm38/Gencode vM23. Because we are analyzing nuclei that contain a significant amount of unspliced mRNA, we identified reads that uniquely and strand-specifically aligned to the entire gene body of each gene (including exons, introns, intron-exon junctions, and exon-exon junctions), assigning an address to each aligned read containing the gene name, cell-identifying barcode sequence, and unique molecular identifier (UMI) extracted from read 1. Next, we demultiplexed the resulting table, correcting sequencing errors in the barcodes as described in Yuan and Sims [Yuan and Sims, Scientific Reports, 2016] to produce a count matrix for each sample.
snDNA-seq and snATAC-seq data were processed using a custom pipeline available here (https://github.com/simslab/dna10x). The pipeline attempts to mimic some of the basic data processing procedures that are implemented in the 10x Genomics Cell Ranger software packages for analysis of snATAC-seq and Multiome data, including the formatting of output files. We generated sample-demultiplexed fastq files using the mkfastq command in cellranger-atac v2.0.0 (10x Genomics). We aligned paired-end reads 1 and 2 to the human or mouse genome using bwa mem v0.7.17-r1188 [Li, arXiv, 2013] after removing a standard adapter sequence (CTGTCTCTTATACACATCT) from each read using cutadapt v2.8 [Martin, EMBnet.journal, 17, 1, 2011].  We then extracted all reads with an alignment score that was >90% of the read length and insert size <1 kb. We also implemented an error correction procedure for the cell-identifying barcodes from read 3. Briefly, for cell-identifying barcodes that do not appear in the standard list provided by 10x Genomics, we first determine the frequency falt of each barcode in the standard list in the data set. For each observed barcode sequence that has a Hamming distance of one from a sequence on the standard list, we estimate the posterior probability palt that the barcode deviates from the standard list due to sequencing error using the quality scores for the putatively errant base provided by Illumina or Element palt = falt10-q/10 where q is the quality score. If palt>0.975 for any alternative barcodes, then we replace the errant barcode with the alternative barcode from the standard list with the highest value of palt. Finally, we establish read addresses for each alignment that passes the filter described above comprised of a cell-identifying barcode, chromosome, a fragment start position, a fragment end position and collapse identical fragments. Finally, we sort the fragments by alignment position on the genome and output a table in the format of the “fragments.tsv” file that is typically produced by Cell Ranger.
Assembly: human-only libraries: GRCh38/Gencode v24; human/mouse mixture: GRCm38/Gencode vM23/GRCh38/Gencode v32
Supplementary files format and content: PTO068_1_2.matrix.txt.gz :gzip-compressed, tab-delimited file containing the scRNA-seq count matrix where each row is a gene (labeled by a gene ID and gene symbol) and each column is a cell (with a header containing the cell-identifying barcode and library ID)
Supplementary files format and content: PTO069_*.fragments.tsv.bz2 :bzip2-compressed, tab-delimited file tabulating the alignment position (chromosome, start, end), cell-identifying barcode, and read count for each unique fragment for genomic data (scATAC-seq, scDNA-seq, DEFND-seq)

organism:
Homo sapiens
Mus musculus

source_name: U87-MG, NIH-3T3

growth_protocol: 3T3 cells (ATCC #CRL-1658) and U87 MG cells (ATCC #HTB-14) were cultured in Dulbecco's Modified Eagle's Medium (ATCC #30-2002) supplemented with 10% feline bovine serum (FBS, ThermoFisher # A3160401). Eagle’s Minimum Essential Medium (ATCC #30-2003) was used to culture BJ cells (ATCC CRL-2522). TrypLE Express Enzyme (ThermoFisher #12605010) was used for dissociating cells during cell passages .

extract_protocol:
snATAC-seq: Nuclei were prepared from cryopreserved BJ fibroblasts. Frozen cells were thawed and added to a Dounce homogenizer containing 1 mL of nuclei isolation buffer (NIB: 10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal (Millipore Sigma #18896), and 1 x protease inhibitors (Millipore Sigma #118735800001)). The sample was gently homogenized on ice with 5 strokes of the loose pestle and 5 strokes of the tight pestle. The cells were transferred to a conical and 5 mL of PBS (Gibco #10010-031) was added. The sample was spun down at 500 g for 5 minutes, washed with 10 mL of PBS and resuspended in 100 µL of 10x Genomics Nuclei Buffer (10x Genomics, #2000207).  xSDS snDNA-seq: Nuclei that were cross-linked and then treated with sodium dodecyl sulfate (SDS) to remove nucleosomes (xSDS) were prepared following Adey et al. Briefly, BJ fibroblasts were washed with 10 mL of PBS and covered in 3 mL of TrypLE (ThermoFisher #12605028) for 10 minutes at 37 °C. Then 9 mL of media was added, quenching the dissociation, and cells were spun down. The cells were resuspended in 10 mL of media with 406 µL of 37% formaldehyde (Millipore Sigma #252549) and gently rotated at room temperature for 10 minutes. 2.5 M glycine (800 µL) was then added and the suspension was incubated on ice for 5 minutes. Cells were centrifuged at 500 g for 8 minutes and washed with 10 mL of PBS. 5 mL of NIB was added to the pellet and the suspension was incubated for 20 minutes at 4 °C under rotation. Cells were then spun down at 500 g for 5 minutes and washed with 900 µL of NEBuffer 2.1 (New England Biolabs #B7202). The cells were pelleted (500 g for 5 minutes) and resuspended in NEBuffer 2.1 with 12 µL of 20% SDS. The solution was placed in a gentleMACS and vigorously shaken at 42 °C for 30 minutes. 200 µL of 10 % Triton-X (Millipore Sigma #T8787) was added and the cells were again shaken at 42 °C for 30 minutes.  LAND snDNA-seq/DEFND-seq: The LAND protocol for adherent cells using 10x reagents was adapted from the LAND protocol. BJ fibroblasts were first washed with 10 mL of PBS and dissociated with 3 mL of TrypLE for 10 minutes at 37 C. Media (9 mL) was used to quench the dissociation reaction and collect the cells. The cells were spun down (300 g for 5 minutes) and 200 µL of DEFND buffer (175 µL NIB, 10 µL 1 mg/mL protease inhibitor (Millipore Sigma #11429868001), 25 µL 100 mM lithium diiodosalicylate (Millipore Sigma #653-14-5)), was added and incubated on ice for 5 minutes. Immediately following this incubation, 10 mL of nuclei isolation buffer was added and the nuclei were centrifuged at 4 °C for 5 minutes at 500 g. The supernatant was removed and 100 µL of 10x Genomics Nuclei Buffer. A fraction of nuclei was stained with SYBR green and counted on a Countess with a GFP filter set.  GBM Cryopreserved Tissue DEFND-seq: A cryopreserved IDH wildtype Grade IV GBM sample was obtained from excess material collected for clinical purposes from de-identified brain tumor specimens. Nuclei were prepared from this anonymous sample according to XXXXX . Frozen tissue was placed in a Dounce homogenizer containing 1 mL of homogenization buffer (HB: 1 µM DTT, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM tris, 1x protease inhibitor, 0.4 U/µL RNAse, 0.2 U/µL SUPERase In) and subjected to 15 strokes using the loose piston and 15 strokes using the tight piston. The homogenate was divided into 5 volumes and each was strained twice. The filtered homogenate was combined into a tube and centrifuged at 1000 g for 10 minutes at 4 °C. The pellet was resuspended in 1000 µL of HB and strained with 4 strainers (250 µL of homogenate for each strainer). The strained homogenate was again combined into a tube and centrifuged at 1000 g for 10 minutes at 4 °C. The pellet was resuspended in 250 µL of HB to which 250 µL of 50% iodixanol dilution media (IDM: 250 mM sucrose, 150 mM KCl, 30 mM MgCl2, 60 mM tris) was added resulting in a 25% IDM/nuclei suspension. This suspension was carefully layered on top of a tube containing 50% IDM at the bottom and 29% IDM at the surface, and centrifuged at 18,000 g for 23 minutes at 4 C. The nuclei formed a white pellet or sheet in the middle of the tube between the layers. All solution around this pellet was removed – first from the top and then from the bottom, and the pellet was resuspended in 1 mL of chilled PBS and centrifuged (500 g for 5 minutes at 4 °C). The supernatant was removed and the pellet was then treated with DEFND buffer for 5 minutes on ice. Immediately following this incubation, 5 mL of NIB with RNAse inhibitors was added at the nuclei were centrifuged at 500 g for 5 minutes at 4 °C.
DEFND-seq/10x Multiome (snRNA/DNA-seq), snATAC-seq, snDNA-seq
snATAC-seq: Single-cell ATAC libraries were prepared with these nuclei using the 10x Genomics Single Cell ATAC kit (10x Genomics #1000176, #1000162, and #1000212) according to the manufacturer’s protocol. xSDS snDNA-seq: The cells were pelleted (500 g for 5 minutes) and resuspended in 100 µL of 10x Genomics Nuclei Buffer, counted, and tagmented following the Chromium Single Cell ATAC protocol. Tagmented nuclei were loaded onto a 10x Chromoium controller and libraries were prepared according to the Chromimum Single Cell ATAC protocol (10x Genomics #1000176, #1000162, and #1000212). LAND snDNA-seq: Nuclei were then tagmented and prepared for single-cell sequencing with the Chromium Single Cell ATAC kit (10x Genomics #1000176, #1000162, and #1000212) and protocol. DEFND-seq: Nuclei were then tagmented and prepared for single-cell sequencing with the Chromium Single Cell Multiome kit (10x Genomics #1000285, #1000230, #1000215).

value: U87-MG, NIH-3T3

tag: cell type

value: glioma cells (U87), fibroblast (3T3)


title: HEK293T_A17


title: snDNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq DNA library - first reaction)


title: HEK293T_A25


title: PADI Library 2, Bin 4


title: PADI Library 2, Bin 3


title: DSSFEV2

city: Shenzhen

first: Ying

last: Wang

address: xinan

department: Shenzhen hospital

country: China

institute: southern mecical university

library_source: transcriptomic

data_processing:
1) Removal of the 3' end of the junction using Cutadapt, with the removed portion having at least a 10 bp Overlap (AGATCGGAAG) to the known junction, allowing for 20% base mismatches;2) Remove Reads with an average mass fraction below Q20
Filtered Reads were aligned to the reference genome using the upgraded version of TopHat2, HISAT2(http://ccb.jhu.edu/software/hisat2/index.shtml) software. HISAT2 uses an improved BWT algorithm that is faster and has a lower resource footprint. HISAT2 uses default parameters for non-strand-specific libraries, and requires the library type to be specified for strand-specific libraries (i.e., use --rna-strandness RF for first, --rna-strandness FR for second).
We analysed expression saturation using RSeQC, i.e.: sequencing results were analysed at 5%, 10%, 15%.... . 100%.The expression of all genes was calculated separately for different sampling ratios (i.e., 20 times for each gene), and then compared with the actual expression to get the relative error.
Assembly: mm10
Supplementary files format and content: expression.xlsx

organism: Mus musculus

source_name: mouse colon

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chainreaction (PCR) amplified.

tag: tissue

value: mouse colon

value: Lamina propria monocytes


title: HEK293T_A15


title: DSS3


title: DSSFEV3


title: HEK293T_A14


title: PADI Library 2, Bin 2


title: DSSFEV1


title: Vector_Day_6_clone 5_biol rep 5

city: Valencia

first: Vicente

middle: Pérez

last: García

address: C/ Eduardo Primo Yúfera

country: Spain

institute: Fundación Centro de Investigación Príncipe Felipe

data_processing:
Reads were mapped to Mus musculus GRCm38 genome  assembly using HISAT2 v2.1.0.
Read counts and normalization were performed with SeqMonk software.
Assembly: GRCm38
Supplementary files format and content: Matrix with raw counts for each sample per column

extract_protocol:
Total RNA was extracted with Trizol followed by Dnase treatment using TURBO DNA-free kit (Life Technologies AM1907).
RNA-seq libraries were generated from 500ng using TruSeq Stranded mRNA library prop (Illumina, 20020594).

value: Trophoblast stem cells

tag: genotype

value: Vector

tag: time point


title: HEK293T_A20


title: Vector_Day_6_clone 4_biol rep 4


title: PADI Library 2, Bin 1


title: PADI Library 2, Bin 12


title: Vector_Day_6_clone 3_biol rep 3


title: HEK293T_A12


title: HEK293T_A13


title: Vector_Day_6_ clone1_biol rep 1


title: Vector_Day_3_clone 5_biol rep 5


title: HEK293T_A11


title: Vector_Day_6_clone 2_biol rep 2


title: Vector_Day_3_clone 4_biol rep 4


title: PADI Library 2, Bin 11


title: HEK293T_A16


title: Vector_Day_3_clone 3_biol rep 3


title: HEK293T_A10


title: Vector_Day_3_clone 2_biol rep 2


title: DSS1


title: PADI Library 1, Bin 9


title: Vector_Day_3_ clone1_biol rep 1


title: PADI Library 1, Bin 8


title: HEK293T_A09


title: HEK293T_A08


title: PADI Library 1, Bin 7


title: Vector_Day_0_clone 5_biol rep 5


title: Vector_Day_0_clone 3_biol rep 3


title: HEK293T_A07


title: Vector_Day_0_clone 2_biol rep 2


title: PADI Library 1, Bin 6


title: Vector_Day_0_ clone1_biol rep 1


title: PADI Library 2, Bin 10


title: Pigl_KO_Day_6_clone 5_biol rep 5


title: PADI Library 1, Bin 5


title: Pigl_KO_Day_6_clone 4_biol rep 4


title: HEK293T_A06


title: Pigl_KO_Day_6_clone 3_biol rep 3


title: Pigl_KO_Day_6_clone 2_biol rep 2


title: HEK293T_A05


title: PADI Library 1, Bin 4


title: Pigl_KO_Day_6_ clone1_biol rep 1


title: Pigl_KO_Day_3_clone 5_biol rep 5


title: PADI Library 1, Bin 3


title: PADI Library 1, Bin 2


title: Vector_Day_0_clone 4_biol rep 4


title: Pigl_KO_Day_3_clone 2_biol rep 2


title: HEK293T_A04


title: PADI Library 1, Bin 1


title: HEK293T_A02


title: HEK293T_A01


title: Pigl_KO_Day_3_ clone1_biol rep 1


title: Pigl_KO_Day_0_clone 4_biol rep 4


title: Pigl_KO_Day_3_clone 4_biol rep 4


title: Pigl_KO_Day_0_clone 5_biol rep 5


title: Pigl_KO_Day_0_clone 3_biol rep 3


title: ARF Evolution Library, Bin 9


title: Pigl_KO_Day_0_clone 2_biol rep 2


title: EU-seq in ESC after  triptolide treatment for 120min rep2

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

data_processing:
Processing EU-seq data Adaptor trimming was performed as described in the RNA-seq section. Bwa meme (version 1.0.4, PMID: 35253835) were used for reads mapping with soft clipping option for supplementary alignments. Low-mapping quality reads (MAPQ < 10) were removed using samtools (version 1.4)89. Reads mapped to rRNA and tRNA regions, obtained from UCSC genome browser, were excluded with Bedtools. The number of reads mapped to defined regions was counted using HTseq. Transcripts with low mapped reads (average reads ≤ 20 between replicates for both control and treatment conditions) were excluded from differential gene expression (DGE) analysis. Log2 fold-changes (FC) were calculated using the DESeq290. Mitochondrial transcript reads were counted in 200b bins and regions where geometric mean counts among datasets > 20 were used for calculating scaling factors by normalizing the median of relative abundance.
Assembly: mm10
Supplementary files format and content: Gene track bigwig files
Library strategy: EU-seq

source_name: E14 mouse ESC

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments (Ying et al., 2002). ESCs were cultured in the standard N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium (Thermo Fisher Scientific), supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1μM PD0325901, 3μM CT-99021 (custom-made by ABCR GmbH, Karlsruhe), 100μM 2-mercaptoethanol, 150μM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), 0.5x N2 supplement (made in house or from Thermo Fisher Scientific.

extract_protocol:
Following 5-EU labelling, cells were quickly washed (1x) with PBS, and immediately lysed in RLT buffer and RNA was prepared using RNeasy Mini Kit (Qiagen). The labelled RNA was subsequently enriched using the Click-iT® Nascent RNA Capture Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
EU-seq libraries were prepared using the NEBNext Ultra kit (NEB) as per manufacturer’s instructions and subsequently sequenced using a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: Cells were treated with DMSO or with 500nM triptolide for 120min. The inhibitor was added prior to or simultaneous to adding 5-ethynyl uridine (5-EU), as specified. Cells were pulse-labelled with 0.5 mM 5-EU for 20 min before sample collection.

value: E14 mouse ESC

value: ESC

tag: treatment

value: Triptolide 500nM treatment for 120min


title: EU-seq in ESC after  triptolide treatment for 120min rep1


title: Pigl_KO_Day_0_ clone1_biol rep 1


title: Pigf_KO_Day_6_clone 5_biol rep 5


title: ARF Evolution Library, Bin 7


title: 3T3_sc24

description: Mixed with HEK293T cells during library construction


title: Pigf_KO_Day_6_clone 4_biol rep 4


title: Pigf_KO_Day_6_clone 3_biol rep 3


title: ARF Evolution Library, Bin 6


title: HEK293T_A03


title: Pigf_KO_Day_6_clone 2_biol rep 2


title: ARF Evolution Library, Bin 5


title: DSS2


title: ARF Evolution Library, Bin 4


title: 3T3_sc22


title: Pigf_KO_Day_3_clone 5_biol rep 5


title: Pigf_KO_Day_6_ clone1_biol rep 1


title: Pigf_KO_Day_3_clone 4_biol rep 4


title: ARF Evolution Library, Bin 8


title: ARF Evolution Library, Bin 3


title: Pigf_KO_Day_3_clone 3_biol rep 3


title: Pigf_KO_Day_3_ clone1_biol rep 1


title: Pigf_KO_Day_3_clone 2_biol rep 2


title: 3T3_sc20


title: Pigl_KO_Day_3_clone 3_biol rep 3


title: ARF Evolution Library, Bin 1


title: 3T3_sc19


title: Pigf_KO_Day_0_clone 2_biol rep 2


title: Pigf_KO_Day_0_clone 3_biol rep 3


title: Pigf_KO_Day_0_clone 5_biol rep 5


title: Pigf_KO_Day_0_clone 4_biol rep 4


title: PADI Library 1, Bin 12


title: Pigf_KO_Day_0_clone 1_biol rep 1


title: 3T3_sc23


title: PADI Library 1, Bin 11


title: MCA fibrosarcoma (9609) tumor derived macrophages, MEK1-hi exosomes treated 2

city: La Jolla

first: Jack

last: Bui

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
usegalaxy.org.  Galaxy is an open source, web-based platform for bioinformatic analyses.  All data processing was performed with Galaxy tools.
All read files were assesed for quality control using FastQC (Galaxy Version 0.73+galaxy0).
Quality checked paired-end reads were aligned with Tophat (Galaxy v 2.1.1) against mm10 reference genome.
Transcript assemblies from aligned reads were created using Cufflinks (Galaxy v 2.2.1.3) using mm10 reference annotation (UCSC genome browser)
All assemblies were merged into a singluar file using Cuffmerge (Galaxy v 0.0.6) and analyzed with Cuffdiff (Galaxy v 2.2.1.6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for both "MEK1 exo" and "GFP exo"

source_name: 9609 parent

extract_protocol:
RNA was harvested using TRIzol reagent
Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0   were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes   (Illumina, San Diego, CA).  Samples were processed following manufacturer's instructoins, starting with 750 ng of RNA and modifying   RNA shear time to five minutes.  Resulting libraries were multiplexed and sequenced with 100 basepair (bp) paired end reads (PE100) to   a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000.  Samples were demultiplexed using bcl2fastq v2.2.0   Conversion Software (Illumina, San Diego, CA).

value: 9609 parent

value: Tumor macrophage

value: WT

value: MEK1-hi exosome


title: 3T3_sc17


title: 3T3_sc16


title: 3T3_sc21


title: MCA fibrosarcoma (9609) tumor derived macrophages, MEK1-low exosome treated 2

value: MEK1-low (GFP) exosome


title: ARF Evolution Library, Bin 12


title: MCA fibrosarcoma (9609 MEK1-hi) tumor derived macrophages 3

data_processing:
usegalaxy.org.  Galaxy is an open source, web-based platform for bioinformatic analyses.  All data processing was performed with Galaxy tools.
All read files were assesed for quality control using FastQC (Galaxy Version 0.73+galaxy0).
Quality checked paired-end reads were aligned with Tophat (Galaxy v 2.1.1) against mm10 reference genome.
Transcript assemblies from aligned reads were created using Cufflinks (Galaxy v 2.2.1.3) using mm10 reference annotation (UCSC genome browser)
All assemblies were merged into a singluar file using Cuffmerge (Galaxy v 0.0.6) and analyzed with Cuffdiff (Galaxy v 2.2.1.6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for both "MEK1_exo" and "GFP_exo"

value: MEK1-hi exosomes


title: ARF Evolution Library, Bin 11


title: 3T3_sc15


title: MCA fibrosarcoma (9609) tumor derived macrophages, MEK1-low exosome treated 1


title: ARF Evolution Library, Bin 2


title: 3T3_sc14


title: MCA fibrosarcoma (9609 MEK1-hi) tumor derived macrophages 2


title: MCA fibrosarcoma (9609 MEK1-hi) tumor derived macrophages 1


title: MCA fibrosarcoma (9609 MEK1-low) tumor derived macrophages 2

source_name: 9609 MEK1-low

value: 9609 MEK1-low

value: MEK1-low (GFP) exosomes


title: 3T3_sc18


title: ARF Evolution Library, Bin 10

value: MATa TF Library x MATalpha Reporter Strain


title: MCA fibrosarcoma (9609 MEK1-low) tumor derived macrophages 1


title: 3T3_sc11


title: 3T3_sc13


title: MCA fibrosarcoma (9609) tumor derived macrophages, MEK1-hi exosomes treated 1


title: RNA: thymocytes

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

data_processing:
We used Cell Ranger v7.0.1 (10X Genomics) pipeline for FASTQ file generation from raw sequencing data.
Raw BCL files from Illumina HiSeqXten were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the Macaca fascicularis reference genome (Macaca_fascicularis_5.0), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
The raw count matrices of 10x genomics were imported into Seurat 4.3.0.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: The lists of cell barcode in tsv format, filtered gene matrix table with raw gene counts in mtx and HDF5 format.

organism: Macaca fascicularis

source_name: thymus

extract_protocol:
Thymus sample for single-cell RNA-seq were obtained from a healthy male rhesus monkey aged 2 years. Thymus tissues were minced into a single-cell suspension using a 70 μm filter and a syringe plunger. And isolated total thymocytes were used for analysis.
Libraries were prepared using the Chromium controller according to the 10x Chromium Next GEM Single Cell 5’ Reagent Kits v2 User Guide (CG000331).

value: thymus

tag: developmental stage

value: young

value: T cell


title: HUVEC, shNSUN2, meRIP-seq [Sh2.IP]

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
HISAT2 software (v2.0.4)
Assembly: Hg 38
Supplementary files format and content: Excexls including differentially expressed genes and differentially methylated mRNA
Library strategy: meRIP-seq

source_name: umbilical cord

extract_protocol:
For RNA-seq, The integrity of total RNA was assessed using a 2100 Bioanalyzer from Agilent Technologies, while the concentration was determined using a Qubit 2.0 fluorometer with the Qubit RNA assay kit from Invitrogen. For meRIP-seq, RNA was randomly fragmented and incubated overnight with protein A/G beads conjugated to m5C antibodies.
For RNA-seq, sequencing libraries were prepared utilizing the Illumina TruSeq RNA Sample Prep Kit (Illumina, USA), and high-throughput sequencing was performed on an Illumina HiSeq 3000 platform (Illumina, USA).  For meRIP-seq, the captured RNA was eluted and extracted using TRIzol reagent. Library construction was performed for both input samples and m5C IP samples. The libraries were assessed using an Agilent 2100 Bioanalyzer (Agilent, USA) and sequenced on a NovaSeq 6000 platform (Illumina, USA). Following quality control and removal of low-quality reads, the clean reads from all libraries were aligned to the reference genome (HG19) using HISAT2 software (v2.0.4).

value: umbilical cord

value: HUVEC

value: NSUN2 konckdown

value: Normal


title: HUVEC, shNSUN2, meRIP-seq [Sh1.IP]


title: PADI Library 10, Bin 8


title: PADI Library 10, Bin 7


title: Patient 9 OSCC10

type: RNA

city: Baltimore

first: Vasileios Ionas

last: Theofilou

state: MD

address: 650 W Baltimore St

department: Oncology and Diagnostic Sciences

institute: School of Dentistry, University of Maryland Baltimore

hyb_protocol: quality control: RNA quality control (QC) analysis was run on nanochip, to ensure required 200nt in 50-300ng with no prior amplification or enzymatic reaction. Hybridization was carried in a regular thermal cycler. The hybridized mix was purified using magnetic beads in the nCounter machine in the institute of genome sciences (IGS) University of Maryland, Baltimore.

scan_protocol: nCounter digital analyser scan with 555FOVs was used and image acquisition was on the ncounter SPRINT system

data_processing: Data analysis was carried using IO-360 platform 770 genes code sets using the nSolver 4.0 software basic and advanced costumed analysis.

label: biotin

source_name: Head and neck cancer

label_protocol: Biotinylated capture probes and color coded reporter probes were used for the hybridization complex, according to the manufacturer's protocol

extract_protocol: Three to five slides of 5 um thick FFPE tissue sections of prospectively collected HNSCC tumor tissue were used for RNA extraction using Rneasy FFPE kit (Qiagen, catalog no 73504). The tumor rich areas and 3-4mm of peritumoral stromal were identified and manually micro-dissected by a surgical oral pathologist (RY) guided by H&E stained section.

value: Oral Squamous cell Carcinoma

tag: age

tag: gender

value: Female

tag: smoking

value: Yes

tag: alcohol

value: No

tag: race

value: Caucasian

tag: location

value: Oral cavity and mobile tongue

tag: Stage

value: IV

tag: prior radiotherapy

tag: prior chemotherapy

tag: histological inflammatory subtype

value: Immune-desert

tag: stromal fibrosis

tag: fibromyxoid stroma

tag: peritumoral stromal fibrosis

tag: peritumoral stromal inflammation


title: Patient 8 OSCC09

tag: tissue

value: Immune-excluded / immune-desert


title: PADI Library 10, Bin 6

tag: cell line

value: MATa TF Library x MATalpha Reporter Strain


title: 3T3_sc9


title: HUVEC, shNSUN2, meRIP-seq [Sh2.Input]

tag: genotype

tag: treatment


title: HUVEC, shNSUN2, meRIP-seq [Sh1.Input]


title: 3T3_sc8


title: 3T3_sc7


title: Patient 7 OSCC08

tag: age

tag: gender

value: Male

value: African American

value: I

value: Immune-excluded


title: HUVEC, shCtrl, meRIP-seq [Control2.IP]

value: umbilical cord

value: HUVEC

value: WT


title: PADI Library 10, Bin 4


title: Patient 5 OSCC6

value: Oral Squamous cell Carcinoma

tag: smoking

tag: alcohol

value: II

value: Inflammed


title: 3T3_sc6


title: 3T3_sc12


title: PADI Library 1, Bin 10


title: Patient 4 OSCC5

value: Yes

value: No

tag: race

tag: location


title: HUVEC, shCtrl, meRIP-seq [Control1.IP]

value: Normal


title: PADI Library 10, Bin 9


title: PADI Library 10, Bin 5


title: Patient 3 OSCC4

value: Female

value: Oral cavity and mobile tongue

tag: Stage

value: IV

tag: prior radiotherapy


title: HUVEC, shCtrl, meRIP-seq [Control2.Input]


title: Patient 2 OSCC3

value: Caucasian

tag: prior chemotherapy

tag: histological inflammatory subtype


title: PADI Library 10, Bin 2

value: MATa TF Library x MATalpha Reporter Strain


title: 3T3_sc4


title: 3T3_sc10


title: HUVEC, shCtrl, meRIP-seq [Control1.Input]


title: Patient 1 OSCC1

value: Male

tag: stromal fibrosis

tag: fibromyxoid stroma


title: 3T3_sc5


title: HUVEC, Hypoxia, RNA-seq [Treated-2]

data_processing:
HISAT2 software (v2.0.4)
Assembly: Hg 38
Supplementary files format and content: Excexls including differentially expressed genes and differentially methylated mRNA

value: Hypoxia


title: HUVEC, Hypoxia, RNA-seq [Treated-1]


title: 3T3_sc3


title: PADI Library 10, Bin 12


title: HUVEC, control, RNA-seq [NC-2]


title: 3T3_sc2


title: HUVEC, ctrl [C_1]

data_processing:
The raw data were aligned to the reference genome using bowtie2 software
Assembly: Hg38
Supplementary files format and content: Excel including all identified reads number
Library strategy: CUT&Tag

extract_protocol:
The endothelial cells were incubated with concanavalin A-coated magnetic beads (Bangs Laboratories, USA) at RT for 10 min. The cells were then incubated with the secondary antibody (Millipore, USA) for 60 minutes, followed by incubation with the pA-Tn5 adaptor complex for an additional 60 minutes at room temperature. Subsequently, they were treated with tagmentation buffer (10mM MgCl2 in Dig-med buffer) for another 60 minutes at 37°C. DNA purification was performed using phenol–chloroform–isoamyl alcohol extraction and ethanol precipitation.
After library amplification, sequencing was carried out using a Illumina NovaSeq 6000 system.

value: PBS


title: HUVEC, ctrl [C_1-igg]

value: umbilical cord


title: PADI Library 10, Bin 11


title: PADI Library 10, Bin 3


title: 3T3_sc1


title: PADI Library 10, Bin 10


title: BAT_GlsKO

status: Public on May 18 2024

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw sequencing files were processed using Cell Ranger v7.0.1 based on the default parameters to demultiplex cell barcodes and generate cell-by-gene expression matrices.
The mm10 mouse genome (refdata-gex-mm10-2020-A) from 10X genomics was used.
We next applied SoupX v1.6.2 and DoubletFinder v2.0.3 to remove ambient RNA contamination and doublets, respectively.
We filtered cells with more than 5% of mitochondrial RNA and excluded HB and mitochondrial genes, ribosomal protein families, MTRNR andMALAT1 for downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: brown adipose tissue

extract_protocol:
Brown and white adipose tissues were isolated from chow diet-fed Glsfl/fl mice and GlsAdipoq-Cre mice (n=5 for each genotype) and flash frozen in liquid nitrogen. Samples from each depot and genotype were pooled for the nuclei isolation. Briefly, frozen samples were minced into 1-2 mm2 pieces and homogenized in 3 mL cold lysis buffer (5 mM CaCl2, 3 mM magnesium acetate (Mg(C2H3O2)2), 2 mM EDTA, 0.5 mM EGTA, 10 mM TrisHCl, 1 mM DTT [all Sigma], 1X protease inhibitor [11836170001, Roche] and 0.2 U/µL RNase inhibitor [10777019, Invitrogen] in nuclease free water) using a gentleMACS Dissociator (Miltenyi Biotec). Subsequently, 3 mL lysis buffer with 0.4% Triton X-100 (X100, Sigma-Aldrich) was added and the tubes were centrifuged briefly. The lysates were filtered through a 70 µm cell strainer (BD Biosciences), the filters were washed with 2 mL lysis buffer and centrifuged at 1000 x g for 5 minutes at 4 °C using a swinging bucket rotor. The pellet was resuspended into 1 mL nuclei buffer (2% BSA in PBS supplemented with 0.2U/µl RNase inhibitor and 1 mM DTT) and filtered through a 35 µm cell strainer. Nuclei were stained with 10 µg/mL DAPI (D9542, Sigma-Aldrich), and positive nuclei were sorted into Eppendorf tubes coated with nuclei buffer. The tubes were centrifuged at 1000 x g for 5 minutes at 4 °C and resuspended into nuclei buffer for counting.
Nuclei suspensions were diluted to a concentration of 1100 nuclei/µL and loaded onto a 10X Chip G (10X Genomics). Chromium Single-Cell v3.1 kit was used to prepare libraries according to the manufacturer’s protocol. The libraries were sequenced on a Nextseq 2000 platform (Illumina).

value: brown adipose tissue

value: adipocyte-specific Gls knockout


title: WAT_NC

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue

value: Cre-negative littermates


title: WAT_GlsKO


title: PTBP1-sh3-KO2

first: haimei

last: wen

address: SongHu road 2005

department: Collaborative Innovation Center of Genetics and Development,

institute: Fudan university

description: PTBP1 sh3 knock down, replicate2

data_processing:
reads were mapped to hg38 using STAR
bam file convert to bw file using deeptools
Assembly: hg38
Supplementary files format and content: bw file for reads peak

molecule: polyA RNA

source_name: Epithelial tissue

growth_protocol: Cells were cultured in DMEM (Gibco) supplemented with 15% (HFF cells) and 10% (HEK293T cells) FBS (Gibco) at 37°C in a humidified, 5% CO2 incubator. When the cell confluence reached about 95%, the cells were sub-cultured at 1:4.

extract_protocol:
Total RNA were isolated with TRIzol reagent according to manufacturer's instructions (Invitrogen, 15596026). Then, RNA was reversely transcribed into cDNA with oligo-(dT)23 VN primer and (or) random hexamers using HiScript II 1st Strand cDNA Synthesis Kit (+gDNA wiper) (Vazyme, R212). Gene expression at the RNA level was quantified by qRT-PCR using 2× SYBR mix (Vazyme, Q711). GAPDH’s RNA expression level served as an internal control.
Total RNA was extracted with TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instruction.

value: Epithelial tissue

value: HFF

tag: cell type

value: Human Fibroblast

value: PTBP1 Knock down

value: PTBP1 sh3 Knock down


title: HUVEC, lactate [L_1-igg]

tag: tissue

value: HUVEC

value: WT

value: Lactate


title: PTBP1-sh2-KO2

description: PTBP1 sh2 knock down, replicate2

tag: cell line

value: PTBP1 sh2 Knock down


title: HUVEC, lactate [L_1]

tag: genotype


title: PTBP1-sh1-KO2

description: PTBP1 sh1 knock down, replicate2

tag: treatment

value: PTBP1 sh1 Knock down


title: PFC_M_CVS_vB12, rep4

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Raw data was quality trimmed and clipped for Illumina universal adapter. Potential sequencing errors were detected and corrected using Rcorrector and rRNA fragments have been depleted using SortMeRNA.
Reads were mapped on GRCm38 (mm10) genome reference using segemehl and quantified on Ensembl v102 derived gene annotation utilizing featureCounts. Variance stabilized counts were inferred by DESeq2.
Assembly: mm10 (Ensembl v102)
Supplementary files format and content: Tab delimited text files include raw, variance stabilized and TPM normalized read counts for each sample.

source_name: Brain

growth_protocol: The mice were bred and provided with standard chow (LASQCdiet Rod16-R, LASvendi GMBH, Soest, Germany), containing 50 mg/kg of vitamin B12. Housing conditions involved a 14L:10D light cycle.

extract_protocol:
RNA extraction involved resuspension in Trizol and chloroform precipitation, followed by washing with isopropanol and 75% ethanol. Subsequently, cDNA conversion was performed using the GoScript™ Reverse Transcriptase kit (#A5001, Promega).
Library was prepared using Novogene NGS RNA Library Prep Set (PT042) according to manufacturer instructions.

treatment_protocol: The CVS protocol comprised 21 days of stress with alternating stressors (tube restraint, tail suspension, or 100 mild electric random foot shocks for 1 h each). Saline and vitamin B12 injections were administered on the last day.

value: Brain

tag: region

value: Prefrontal cortex

value: chronic variable stress, vitamin B12

tag: strain

tag: Sex

value: male


title: PTBP1-sh1-KO1

description: PTBP1 sh1 knock down, replicate1


title: PTBP1-sh2-KO3

description: PTBP1 sh2 knock down, replicate3


title: PTBP1-sh2-KO1

description: PTBP1 sh2 knock down, replicate1


title: PADI Library 10, Bin 1

value: MATa TF Library x MATalpha Reporter Strain


title: PFC_M_CVS_vB12, rep2


title: PFC_M_CVS_vB12, rep1


title: control2

description: Control, replicate2

value: Control


title: HUVEC, control, RNA-seq [NC-1]

value: umbilical cord

value: Normal


title: control1

description: Control, replicate1

value: Epithelial tissue

value: HFF


title: PTBP1-sh3-KO1

description: PTBP1 sh3 knock down, replicate1

value: Human Fibroblast

value: PTBP1 Knock down


title: PFC_M_naive_vB12, rep3

value: naive, vitamin B12


title: PFC_M_CVS_vB12, rep3


title: Whole Bone Marrow, Mouse 3332, NPM1cA/SMC3+/-, Rep1

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

data_processing:
BasepairTech
Expression Count and Alignment using STAR aligned to mm9
Differential Expression Analysis using DESeq2
Assembly: mm9
Supplementary files format and content: RawCounts.csv, GCT files (DESeq)

source_name: Whole bone marrow

extract_protocol:
Myeloid sarcoma tumors were collected en masse and dissected away from surrounding tissue and directly placed in Trizole reagent with total RNA isolation and polyA mRNA isolation using NEBNext Poly(A) mRNA magnetic isolation module (NEB, E7490); Whole bone marrow was collected from tibias, femurs and pelvic bones by crushing in PBS buffer (containing 1% pen/strep, 0.5%FBS, and 0.5mM EDTA). Filtered through 70uM filter then spun down and red blood cells were lysed with Red Blood Cell Lysis Buffer, washed with additional PBS buffer, strained through 40uM filter and spun down. Cells were resuspended in PBS buffer and placed in Trizole reagent. Total RNA isolated and polyA mRNA isolation using NEBNext Poly(A) mRNA magnetic isolation module (NEB, E7490).
Libraries were constructed using polyA mRNA magnetic isolation module (NEB, E7490), ERCC RNA Spike-In Mix (ThermoFisher Scientific, 4456840) was added, followed by NEBNext Ultra II RNA library prep kit for Illumina (NEB, E7770), the NEBNext multiplex oligos for Illumina set 1 and set 2 (NEB, E7335 and E7500) and Ampure XP Magnetic Beads (Beckman Coulter, A6388). Libraries quantified using NEBNext lirary quant kit for Illumina (NEB, E7630). PhiX control v3 (Illumina, 15017666)

value: Whole bone marrow

tag: animal id

value: Mouse 3332


title: Myeloid Sarcoma, Mouse 2721, NPM1cA/SMC3+/-, Rep2

source_name: Myeloid sarcoma tumor

value: Myeloid sarcoma tumor

value: Mouse 2721


title: Myeloid Sarcoma, Mouse 1268_1270, NPM1cA/SMC3+/-, Rep1


title: PFC_M_naive_vB12, rep4

value: Brain


title: Myeloid Sarcoma, Mouse 2721, NPM1cA/SMC3+/-, Rep1


title: PFC_M_naive_vB12, rep1

value: Prefrontal cortex


title: PFC_M_CVS, rep4

value: chronic variable stress


title: PFC_M_CVS, rep3

value: male


title: Myeloid Sarcoma, Mouse 1267, NPM1cA/SMC3+/-, Rep1

value: Mouse 1267


title: Whole Bone Marrow, Mouse 2721, NPM1cA/SMC3+/-, Rep1


title: PFC_M_CVS, rep2


title: Whole Bone Marrow, Mouse 1267, NPM1cA/SMC3+/-, Rep1


title: PFC_M_CVS, rep1


title: PFC_M_naive, rep3

value: naive


title: control3

description: Control, replicate3

value: WT

value: Control


title: Myeloid Sarcoma, Mouse 948, NPM1cA/SMC3+/-, Rep2

value: Mouse 948


title: PFC_M_naive, rep2


title: Whole Bone Marrow, Mouse 949, NPM1cA/SMC3+/-, Rep1

value: Mouse 949


title: PFC_M_naive, rep4


title: Whole Bone Marrow, Mouse 1103, NPM1cA/SMC3+/-, Rep1

value: Mouse 1103


title: Myeloid Sarcoma, Mouse 948, NPM1cA/SMC3+/-, Rep1


title: Whole Bone Marrow, Mouse 919, NPM1cA/SMC3+/-, Rep1

value: Mouse 919


title: PFC_M_naive, rep1


title: Myeloid Sarcoma, Mouse 841, NPM1cA, Rep1

value: Mouse 841


title: Transformed_8

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St. LRB525

department: Molecular, Cell & Cancer Biology

institute: UMass Medical School

data_processing:
RNA-seq reads were aligned to the Mus musculus reference genome mm10/GRCm38.p5 (Ensembl GRCm38.89) using STAR (version 2.5.3a) with the following explicit option settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10000 --alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical
The resulting BAM files were sorted by read names and processed by using MMR (Kahles  et al., 2016) to assign multi-mapper reads to their most likely genomic locations.
The BAM files output by MMR were input to featureCounts (version 1.5.3) to generated a gene-level count summary table with the following explicit option settings –d 35 –t exon –M and the GTF file for the reference genome mm10/GCRm38.89 as the genome annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table in a matrix format: column 1 is the GeneID; the others are raw count per gene generated by featureCounts.

source_name: Ba/F3 transformed with U2AF35(S34F)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Immortalized pro-B cells

tag: genotype/variation

value: transformed with U2AF35(S34F)


title: Whole Bone Marrow, Mouse 779, NPM1cA/SMC3+/-, Rep1

value: Whole bone marrow

value: Mouse 779


title: Transformed_6


title: Transformed_7


title: Whole Bone Marrow, Mouse 737, NPM1cA/SMC3+/-, Rep1

value: Mouse 737


title: Whole Bone Marrow, Mouse 782, NPM1cA/SMC3+/-, Rep1

value: Mouse 782


title: PFC_M_naive_vB12, rep2

value: Brain

value: Prefrontal cortex

value: naive, vitamin B12


title: WT NOD

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: 10x genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using cell ranger software v7.0.1
Assembly: mm10
Supplementary files format and content: tab separated value and matrix files

source_name: pancreatic islets

extract_protocol:
Following clamping of the bile duct leading to the duodenum, 5 ml of type XI collagenase (0.4 mg/ ml; Sigma Aldrich) in isolation buffer (1x HBSS, 10 mM HEPES, 1 mM MgCl2; pH 7.4) was injected through the common bile duct to perfuse the pancreas. The inflated pancreas was carefully removed and digested at 37°C for 12-14 min. Crude islets were collected and washed several times with the wash buffer (1x HBSS, 10 mM HEPES, 1 mM MgCl2, 1 mM CaCl2; pH 7.4). Islets were hand-picked under a dissection microscope. Purified islets were then dispersed into single cell suspension using a non-enzymatic cell dissociation solution (Sigma Aldrich) for 3 min at 37°C. Intra-islet live CD45+CD31- cells were sorted using islets from 12-week-old female NOD and NOD.Cxcl16-/- mice.
Libraries for single-cell gene expression and sequencing were prepared at the McDonnell Genome Institute (MGI) at Washington University using the 3v3.1 methods. Specifically, cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.

value: pancreatic islets

value: female

value: Immune cells

value: NOD


title: Transformed_5


title: HT1080_LT_A  LONG TELOMERE REPLICATE 1

city: New Delhi

first: Shantanu

last: Chowdhury

state: Delhi

address: Mathura Road

department: Functional Genomics

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

description:
TruSeq RNA Library Prep Kit v5
HT1080_LT_A

data_processing:
Raw Illumina sequencing reads were checked for quality using FastQC (version 0.11.9) followed by adapter clipping and trimming using Trimmomatic (version 0.39) with default parameters.
Trimmed reads were then aligned to the human reference genome (GRCh38, GENCODE v36) using STAR aligner (version 2.7.8a). Quality checks were performed at each step using the MultiQC tool (version 1.10.1).
FeatureCounts (subread package version 2.0.1) was used to quantify gene expression.  Differential gene expression analysis was performed using the DESseq2 package (version 1.30.0) in R (version 4.0.3). The analysis was performed by removing the effects of confounding variables such as batch and replicate using the appropriate design formula.
Gene expression was normalized using variant stabilizing transformation (vst) for visualization purposes. Genes with BH-adjusted p value < 0.05 and absolute Log2 fold change greater than 1 (at least 100% fold change in either direction) were taken as significantly differentially expressed.
Assembly: hg 38(GRCh38)
Supplementary files format and content: tab delimited text file containg normalized counts (RPKM) for all samples.

source_name: connective tissue

growth_protocol: cells grown in MEM supplemented with 10% FBS at 5% CO2 and 37 degrees

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Invitrogen, Life Technologies) according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols.TruSeq RNA Library Prep Kit v2 was used from preparation of libraries for sequencing

treatment_protocol: no treatment

value: connective tissue

value: fibrosarcoma

value: immortalized

tag: source

value: gift from J.Lingner

value: TERT and TERC constitutively over-expressed


title: HT1080_LT_C LONG TELOMERE REPLICATE 3

description:
TruSeq RNA Library Prep Kit v7
HT1080_LT_C


title: HT1080_C SHORT TELOMERE REPLICATE 3

description:
TruSeq RNA Library Prep Kit v4
HT1080_C

value: ATCC

value: wild type


title: Transformed_4

value: Immortalized pro-B cells

value: transformed with U2AF35(S34F)


title: HT1080_B  SHORT TELOMERE REPLICATE 2

description:
TruSeq RNA Library Prep Kit v3
HT1080_B


title: AML-12 cells, overexpression, GM47544-3

city: Wuhan

first: Qianqian

last: Xiao

address: 1095# Jiefang Ave., Wuhan 430030 People’s Rep. of China

department: Departments of Internal Medicine

institute: Tongji Hospital

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNA-seq reads were aligned to the mm10 genome using STAR.
Read count extraction  were performed using HTSeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: AML-12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Trizol reagent.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hepatocyte

value: GM47544 overexpressed


title: PTBP1-sh3-KO3

description: PTBP1 sh3 knock down, replicate3

value: Epithelial tissue

value: HFF

value: Human Fibroblast

value: PTBP1 Knock down

value: PTBP1 sh3 Knock down


title: Parental_2

source_name: parental Ba/F3

value: Parental (U2AF35-WT)


title: Parental_3


title: NOD.Cxcl16-/-

description: 10x genomics

value: pancreatic islets

value: female

value: Immune cells


title: HT1080_A  SHORT TELOMERE REPLICATE 1

description:
TruSeq RNA Library Prep Kit v2
HT1080_A

value: connective tissue

value: fibrosarcoma

value: immortalized


title: AML-12 cells, overexpression, GM47544-2


title: MDA-MB-231 cells, RCCs,rep2

first: Yang

last: Dong

state: 上海

address: Shanghai

institute: Tongji University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: tab-delimted text file includes raw counts for each sample
Supplementary files format and content: tab-delimted text file includes RPKM counts for each sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM, high glucose supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 1.0 μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: MDA-MB-231 cells were labeled with PKH26 and chased for 12 days. Cells with top 1% PKH26 retaining were sorted as slow-cycling cells (SCCs). Cells with moderate PKH26 intensity were sorted as rapid-cycling cells (RCCs).

value: triple-negative breast cancer (TNBC) cell line

value: WT

value: sorted PKH26lo cells


title: MDA-MB-231 cells, RCCs,rep3


title: Parental_1

value: Immortalized pro-B cells


title: MDA-MB-231 cells, RCCs,rep1


title: MDA-MB-231 cells, SCCs,rep3

value: sorted PKH26hi cells


title: MDA-MB-231 cells, SCCs,rep2


title: AML-12 cells, control, pLKO.1-3

value: hepatocyte


title: MDA-MB-231 cells, SCCs,rep1


title: BAT_NC

value: brown adipose tissue

value: Cre-negative littermates


title: AML-12 cells, overexpression, GM47544-4

value: GM47544 overexpressed


title: AML-12 cells, control, pLKO.1-4


title: MDA-MB-231 cells, H2B-eGFP+ SCCs

treatment_protocol: TetOn-H2BeGFP transducted MDA-MB-231 cells were induced with 5 μg/ml doxycycline for 3 days, and labeled with Claret and Violet and chased for 12 days. Cells with top 1% Claret retaining, top 1% eGFP retaining, top 1% Violet retaining were sorted separately as 3 different subpopulations of slow-cycling cells (SCCs). Bulk cells control were sorted without gating on any fluorescence intensity.

value: TetOn-H2BeGFP tranducted

value: sorted Violet+ cells


title: AML-12 cells, control, pLKO.1-2


title: MDA-MB-231 cells, Violet+ SCCs

value: sorted un-gated cells


title: MDA-MB-231 cells, Claret+ SCCs

value: sorted eGFP+ cells


title: AML-12 cells, control, pLKO.1-1


title: MDA-MB-231 cells, Bulk

value: sorted Claret+ cells


title: HT1080_LT_B  LONG TELOMERE REPLICATE 2

description:
TruSeq RNA Library Prep Kit v6
HT1080_LT_B

value: connective tissue

value: gift from J.Lingner

value: TERT and TERC constitutively over-expressed


title: biochemical filter cotton+water of aquaculture system from the control group,rep3

city: Guangzhou

first: Yarong

last: Liu

state: Guangzhou/Guangdong

address: No. 1 Xingyu Road

department: Aquaculture and Nutrition Research Lab

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

hyb_protocol: 0.6 ug of Cy3-labelled cRNA(specific activity >10.0 pmol Cy3/μg cRNA) wasfragmented at 60'C for 30 minutes in a reaction volume of 22.5ul containing 1xAgilent fragmentation buffer and2xAgilent blocking agent following themanufacturers' instructions. On completion ofthe fragmentation reaction, 22.5ul of2x Agilent hybridization buffer was added to the fragmentation mixture andhybridized to Agilent Human Gene xpression (8*60K)for 17 hours at 65°c in arotating Agilent hybridization oven. After hybridization, microarrays were washed 1minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°CGE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The scanned images were analyzed with Feature xtraction Software 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatiallydetrended Processed Signal intensities as the raw data, Raw data were normalizedin quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2samples flagged as Detected were maintained.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatiallydetrended Processed Signal intensities as the raw data. Raw data were normalizedin quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2samples flagged as Detected were maintained.

organism: wastewater metagenome

source_name: Poly-3-Hydroxybutyrate, 4g/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-ColorLow RNA Input Linear Amplification PLUs kit(Agilent)according to themanufacturer's instructions, followed by RNAeasy column purification (QIAGEN,Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDropND-1000 Spectrophotometer.

growth_protocol: PHB was added at 0 g L-1 and 4 g L-1

extract_protocol: RNA was extracted by mirVanaTM RNA lsolation Kit (Applied Biosystem p/nAM1556 ) following the manufacturer's instructions.

tag: group


title: AML-12 cells, overexpression, GM47544-1


title: biochemical filter cotton+water of aquaculture system from the control group,rep2


title: EA.hy926 cell treated to OA 3

city: Incheon

first: Jeong-In

last: Park

address: 119, Academy-ro

institute: Incheon National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: endothelial

growth_protocol: The EA.hy926 cell line (human vascular endothelial cell line) was cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco®, USA) supplemented with 10% fetal bovine serum (FBS; Gibco®, USA), 1% Penicillin/Streptomycin (P/S; Gibco®, USA), 3.7 g/L sodium bicarbonate (Sigma-Aldrich, USA), 1 mM sodium pyruvate (Gibco®, USA) and maintained at 37℃ under 5% CO2. The cells were grown in a 100 mm culture dish and subcultured every 3 d by detaching with 0.25% (w/v) trypsin-EDTA (Gibco®, USA) at a split ratio of approximately 1:3.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: EA.hy926 cells were seeded at a density of 20×104 cells per well in 96-well plates and incubated for 24 h. Cells were exposed to OA (National Research Council, Canada) at concentrations of 4.0625–1040 nM, respectively. DMEM was used as a solvent for OA.

value: endothelial

value: somatic cell hybrid

value: OA(Okadaic acid)


title: Control of EA.hy926 cell treated to OA 3


title: EA.hy926 cell treated to OA 2


title: Control of EA.hy926 cell treated to OA 1


title: Control of EA.hy926 cell treated to OA 2


title: Precancerous liver tissues, Hras12V transgenic mice, female, 15-month

city: DaLian

first: aiguo

last: Wang

address: DaLian

institute: Dalian Medical University

description: P

data_processing:
fastx (version:0.0.13)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastx (version:0.0.13) (parameter- Quality limit: 0.01).
Trimmed sequence reads were mapped to GrCM38/mm10 using tophat (version:2.0.9) (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using cufflink (version:2.1.1).
Differential genes analysis was performed using cuffdiff.
Assembly: mm10
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes count and FPKM values for each Sample.

source_name: Precancerous liver

extract_protocol:
RNA was harvested using mir VanaTM miRNA Isolation kit (Cat# AM1561, Ambion). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit following manufacturer's protocols.

value: Precancerous liver

value: Hras12V transgenic

value: Female

tag: age

value: 15 months


title: Liver tumor tissues, Hras12V transgenic mice, female, 15-month

description: T

source_name: Liver Tumor (HCC)

value: Liver Tumor (HCC)


title: biochemical filter cotton+water of aquaculture system from the control group,rep1


title: K562 capture EM-seq

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description: K562 DNA methylome profile generated using the Twist Human Methylation Panel

data_processing:
BISCUIT standard processing, minimum coverage 5 is used to derive the average methylation levels in the bedGraph files.
Assembly: hg38
Supplementary files format and content: bedGraph of average methylation levels
Library strategy: EM-seq

growth_protocol: 1 – 4 x 10^6 cells were plated and cultured for 6 days with fresh media added 2 – 3 days. K562 cells were cultured in Iscove's Modified Dulbecco's Medium (30–2005, ATCC), 10% Fetal Bovine Serum (FBS) (45000–736, Gibco), and 1% penicillin/streptomycin (15140122, Gibco). LNCaP cells were cultured in Roswell Park Memorial Institute Medium (RPMI-1640) (30–2001, ATCC), 10% FBS, and 1% penicillin/streptomycin (15140122, Gibco). GM12878 cells were cultured with RPMI-1640 (72400047, Invitrogen), and 15% Fetal Bovine Serum (Gibco, 45000–736), 1% GlutaMAX™ (Gibco, 35050061), and 1% penicillin/streptomycin (15140122, Gibco). HCT116 cells were cultured in McCoy’s 5a medium modified (ATCC,30-2007), 10% Fetal Bovine Serum (FBS) (45000–736, Gibco), and 1% penicillin/streptomycin (15140122, Gibco). All cells were maintained in a 37 °C incubator with 5% CO2 and cultured at a 75 cm2 culture flask (Fisher, BD353136)

extract_protocol:
Genomic DNA from the GM12878, K562, and HCT116 cell lines were extracted according to the QIAGEN QIAmp Mini Kit Protocol.
The three samples were then mechanically sheared to 300 base pairs using the M220 Focused-ultrasonicator (Covaris, 500295), along with methylated lambda control DNA. 200ng of each sample was enzymatically converted using the NEBNext® Enzymatic Methyl-seq Kit (NEB, E7120) with the manufacturer’s protocol. The samples were then indexed during PCR amplification during PCR amplification using EM-Seq™ index primers (NEB 7140). The indexed libraries (200 ng each) were pooled and used as input for the Twist NGS Methylation Detection System for target enrichment. A pre-hybridization solution of blockers and enhancers was created to prepare the pool for hybridization (Twist Bioscience, 104180). The DNA was hybridized with the Twist Human Methylome Panel (Twist Bioscience, 105520), and the targets were bound with streptavidin beads (Twist Bioscience, 100983), followed by a post-capture amplification. The enriched libraries were sequenced to 20X on the Illumina Novaseq PE150 platform.


title: Normal liver tissues, wild-type C57BL/6 mice, female, 15-month

description: W

source_name: Normal liver

value: Normal liver

value: WT


title: EF 3

city: Boston

first: Maria

last: Trojanowska

address: 75 E. Newton St.

department: Arthritis and Autoimmune Diseases Research Center

institute: Boston University

description: Gene expression data from lymphatic cells treated with siERG+siFLI1.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

source_name: lymphatic cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: The cells were grown and maintained in Endothelial Cell Basal Medium MV2 with supplements (PromoCell, Heidelberg, Germany) until they reached 70% confluency

extract_protocol: After 24-hour transfection, total RNAs were extracted with Trizol according to the manufacturer's instructions.

treatment_protocol: The cells were transfected with 10 nM of scrambled siRNA (siSCR), siRNA against ERG (siERG), siRNA against FLI1 (siFLI1), or siRNAs against both siERG and siFLI1 (siEF) using Invitrogen™ Lipofectamine™ RNAiMAX Transfection Reagent for 24 hours.

value: lymphatic cells

tag: sirna


title: Precancerous liver tissues, Hras12V transgenic mice, male, 9-month

description: MP

value: Male

value: 9 months


title: biochemical filter cotton+PHB+water of aquaculture system from the control group,rep3

source_name: Poly-3-Hydroxybutyrate, 0g/L


title: biochemical filter cotton+PHB+water of aquaculture system from the control group,rep2


title: EF 2


title: Liver tumor tissues, Hras12V transgenic mice, male, 9-month

description: MT


title: EF 1


title: GM12878 capture EM-seq

description: GM12878 DNA methylome profile generated using the Twist Human Methylation Panel


title: EA.hy926 cell treated to OA 1


title: Normal liver tissues, wild-type C57BL/6 mice, male, 9-month

description: MW


title: Batch3 UXT cko2 + cGAMP

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed RNA in UXT-CKO BMDM after cGAMP stimulation

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: BMDM cells

growth_protocol: C57BL/6 mice were purchased from the Model Animal Research Center of Nanjing University. The mice were maintained under specific pathogen-free (SPF) conditions at the Center for New Drug Safety Evaluation and Research, China Pharmaceutical University. The MEF cell line was obtained from the American Type Culture Collection (ATCC) and maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) under a humidified atmosphere of 5% CO2 at 37°C. Cultured cells were released by trypsin and passaged every 2 days.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen). Total RNA was extracted using the Trizol reagent (Invitrogen) and prepared into cDNA library according to the standard Illumina RNA-seq instruction.
The cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

treatment_protocol: The Uxt conditional knocking-out mice were generated by mating between LysM-Cre and Uxtflox/flox mice.  Uxtflox mice were generated with CRISPR/Cas9-mediated homologous recombination of a 2289bp double stranded DNA donor containing two loxP sites flanking exon 3. BMDMs (bone marrow-derived macrophages) were prepared from WT and myeloid-cell-specific Uxt-deficient mice (Uxtfl/flCre).   cGAMP was used to stimulate the cGAS-STING signaling specifically in MEF and BMDM cells.

value: primary cell

value: UXT-CKO BMDM

tag: stimulation

value: cGAMP


title: Batch3 UXT cko1 + cGAMP


title: KTC1 cells,TGFBR3 _Over-expression-3,rep3

city: Guang Zhou

first: zhang

middle: han

last: rong

state: Guang dong Province

address: Zhong shan Second Road

institute: The First Affiliated Hospital of SunYat-sen University

data_processing:
RNA mapping:In this RNA-SEQ data analysis process, we used Hisat2 as the RNA mapping algorithm to compare the filtered clean data to the sequenced species (Taxonomy ID: 9606) on the corresponding reference genome (GRCh38) to determine the location of sequencing sequences on the genome.
Expression statistics:According to the results of RNA Mapping and genome annotation file (detailed recording of the location information of each gene on the chromosome), HTSeq algorithm was used to calculate the expression of each gene.
We applied DESeq2 algorithm [Love M I , Huber W , Anders S . Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2[J]. Genome Biology, 2014, 15(12):550.] to filter the differentially expressed genes, after the significant analysis, P-value and FDR analysis [Benjamini Y, et al. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001 Nov 1;125(1-2):279-84.] were subjected to the following criteria: i) Fold Change>2 or < 0.5; ii) ,P-value<0.05,FDR<0.05.
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of the differentially expressed genes in the experiment. [Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories (P-value < 0.05).
Pathway analysis was used to find out the significant pathway of the differentially expressed genes according to KEGG database. We turn to the Fisher’s exact test to select the significant pathway, and the threshold of significance was defined by P-value< 0.05. [Draghici S, et al. A systems biology approach for pathway level analysis. Genome Res. 2007 Oct;17(10):1537-45. Epub 2007 Sep 4.]
Assembly: GRCh38.Ensembl104
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: Thyroid

extract_protocol:
Add 200ul chloroform for every 1mlTRIzol, swirl and mix for 30 seconds, and let stand at room temperature for 3 minutes; Then centrifuge (4℃, 12000g×15 min) and slowly draw the upper water phase to the new 1.5ml EP tube. Add 500ul isopropyl alcohol for every 1ml of TRIzol, mix upside down, and let stand at room temperature for 10 minutes; After centrifugation, the supernatant was discarded (4℃, 12000g×10 min) to obtain RNA precipitation: the EP tube was inverted on the toilet paper and placed in a ventilated place to dry the RNA precipitation. Every 1ml of TRIzol was added with 1ml 75% ethanol, and then blown and mixed well. After centrifugation, discard the supernatant (4℃, 7500g×5 minutes), reverse the EP tube on the toilet paper, and place it in the fume hood to dry. Add nuclease-free water and mix well. Then heat at 55-60℃ for 10 minutes. The concentration and purity of RNA were determined by ultraviolet spectrophotometer to determine the light absorption of total RNA at 260nm and 280nm wavelengths.
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by NovaSeq 6000 on a 150 bp paired-end run.

value: Thyroid

value: Papillary thyroid cancer cells

value: Overexpression TGFBR3


title: Batch3 UXT WT2 + cGAMP

description: expressed RNA in BMDM cells after cGAMP stimulation


title: Batch3 UXT WT1 + cGAMP

description: expressed RNA in BMDM after cGAMP stimulation


title: KTC1 cells,TGFBR3 _Over-expression-2,rep2


title: Batch2 UXT ov2 + cGAMP

description: expressed RNA in UXT overexpression MEF cells after cGAMP stimulation

source_name: MEF cell lines

value: mouse embryo fibroblasts

value: UXT overexpression


title: HCT116 capture EM-seq

description: HCT116 DNA methylome profile generated using the Twist Human Methylation Panel


title: Fli 1

description: Gene expression data from lymphatic cells treated with siFLI1.


title: KTC1 cells,TGFBR3 _Over-expression-1,rep1


title: KTC1 cells,Empty_vector-3,rep3

value: Empty Vector


title: Batch2 UXT WT2 + cGAMP

description: expressed RNA in MEF cells after cGAMP stimulation


title: Batch2 UXT WT1 + cGAMP


title: Batch2 UXT ov1 + cGAMP


title: KTC1 cells,Empty_vector-2,rep2


title: Batch1 UXT si2 + cGAMP

description: expressed RNA in UXT knockdown MEF cells after cGAMP stimulation

value: UXT knockdown


title: biochemical filter cotton+PHB+water of aquaculture system from the control group,rep1


title: KTC1 cells,Empty_vector-1,rep1


title: Batch1 UXT WT2 + cGAMP


title: Batch1 UXT si1 + cGAMP


title: Batch1 UXT WT1 + cGAMP


title: nasal_epithelial_cell, 6af2_4cd1

status: Public on May 17 2024

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58th Street, CLSC 501

department: Human Genetics

institute: The University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Asthma&Allergy Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using standard Illumina scanner settings.

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5%) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using ENmix. Please see https://github.com/hansenlab/IlluminaHumanMethylationAllergymanifest/tree/4a00cd62600a662f9a5f1cd32b5aeecee87225a8 for annotation and manifest packages.
MatrixProcessed.txt:  ENmix normalized Beta values
SignalIntensities.txt:  Unmethylated and methylated signal intensities after background normalization.

label: Cy5, Cy3

label_protocol: Standard Illumina protocol.

extract_protocol: Flocked nasal swabs were obtained at age 5-7 years and samples were stored at -80, then extracted using AllPrep DNA/RNA kit (Qiagen) following the manufacturer's protocol.

value: female

tag: proportionpositiveskinpricktests

tag: plate

tag: ageindays

tag: cohort (the year of sample recruitment)

tag: array


title: ERG 1

description: Gene expression data from lymphatic cells treated with siERG.

tag: cell type

value: siERG


title: nasal_epithelial_cell, ce8e_4773

value: male

value: hispanic


title: nasal_epithelial_cell, 7840_4c91


title: ERG 3

value: lymphatic cells


title: nasal_epithelial_cell, a8a7_4afe


title: nasal_epithelial_cell, 0073_4dfe


title: nasal_epithelial_cell, e857_48df


title: nasal_epithelial_cell, 0408_4bbf


title: nasal_epithelial_cell, b79c_4b0a

value: multiple


title: nasal_epithelial_cell, 8343_46b6


title: SCR 3

description: Gene expression data from lymphatic cells treated with scrambled siRNA.

value: scrambled siRNA


title: SCR 2


title: ERG 2


title: nasal_epithelial_cell, 3232_4bf1


title: nasal_epithelial_cell, b270_4af8


title: nasal_epithelial_cell, e18e_4b0a


title: Fli 2


title: nasal_epithelial_cell, c7cd_4927


title: nasal_epithelial_cell, 860e_4ca1


title: nasal_epithelial_cell, 71d5_4589


title: nasal_epithelial_cell, acb2_4dcf


title: Fli 3


title: nasal_epithelial_cell, 7edf_4a68


title: nasal_epithelial_cell, 477f_4f46


title: nasal_epithelial_cell, 2b33_4d5a


title: SCR 1


title: nasal_epithelial_cell, 9b99_41ca


title: nasal_epithelial_cell, b448_4fef


title: nasal_epithelial_cell, f72e_4bbe


title: nasal_epithelial_cell, 254f_4582


title: nasal_epithelial_cell, ad78_4db0


title: nasal_epithelial_cell, ae6e_4914


title: nasal_epithelial_cell, 320f_4297


title: nasal_epithelial_cell, 9b2c_4a78


title: nasal_epithelial_cell, ab54_4a11


title: nasal_epithelial_cell, acf1_4261


title: nasal_epithelial_cell, d4ee_40d2


title: nasal_epithelial_cell, fdd1_48fd


title: nasal_epithelial_cell, 6ef8_4a1c


title: nasal_epithelial_cell, 3d24_45ff


title: nasal_epithelial_cell, 5bb8_4eed


title: nasal_epithelial_cell, 59be_4703


title: nasal_epithelial_cell, 14d8_4fe1


title: nasal_epithelial_cell, 8937_4ce2


title: nasal_epithelial_cell, f475_4688


title: nasal_epithelial_cell, 8740_4fbf


title: nasal_epithelial_cell, 996d_4f8a


title: nasal_epithelial_cell, 65ca_4413


title: nasal_epithelial_cell, 150b_4a39


title: PTBP1-sh1-KO3

description: PTBP1 sh1 knock down, replicate3

source_name: Epithelial tissue

tag: tissue

value: Epithelial tissue

tag: cell line

value: HFF

value: Human Fibroblast

tag: genotype

value: PTBP1 Knock down

tag: treatment

value: PTBP1 sh1 Knock down


title: nasal_epithelial_cell, d235_4e28

tag: Sex


title: nasal_epithelial_cell, 5706_4587


title: nasal_epithelial_cell, 4c7c_4c61


title: nasal_epithelial_cell, 162b_4c53


title: nasal_epithelial_cell, 3477_4e83


title: nasal_epithelial_cell, e90a_4de4


title: nasal_epithelial_cell, 8e33_4e93


title: nasal_epithelial_cell, 914a_475d


title: nasal_epithelial_cell, 27af_4fda


title: nasal_epithelial_cell, fdcb_4986


title: nasal_epithelial_cell, d8bd_45bf


title: nasal_epithelial_cell, e240_4088


title: nasal_epithelial_cell, 6217_4c9e


title: nasal_epithelial_cell, c366_4279


title: nasal_epithelial_cell, 89f4_42d4


title: nasal_epithelial_cell, e233_4b9a


title: nasal_epithelial_cell, 6c97_46fb


title: nasal_epithelial_cell, bd3f_4dc9


title: nasal_epithelial_cell, cf31_4b4d


title: nasal_epithelial_cell, 9286_41e8


title: nasal_epithelial_cell, d1e5_4127


title: nasal_epithelial_cell, e2c4_4e45


title: nasal_epithelial_cell, 04ce_4a2e


title: nasal_epithelial_cell, 7392_42a1


title: nasal_epithelial_cell, 02be_4b5c


title: nasal_epithelial_cell, 6713_497f


title: nasal_epithelial_cell, 2efb_496f


title: nasal_epithelial_cell, ac61_4adc


title: nasal_epithelial_cell, 7639_41c4


title: nasal_epithelial_cell, 310a_48ed


title: nasal_epithelial_cell, 36a9_4643


title: nasal_epithelial_cell, 671f_46b0


title: nasal_epithelial_cell, cd7e_4851


title: nasal_epithelial_cell, dda0_428a


title: nasal_epithelial_cell, f48d_4a90


title: nasal_epithelial_cell, d645_41c6


title: nasal_epithelial_cell, deed_4234


title: nasal_epithelial_cell, f7c7_4572


title: nasal_epithelial_cell, c00b_4d69


title: nasal_epithelial_cell, 1bba_4290


title: nasal_epithelial_cell, 4166_4d44


title: nasal_epithelial_cell, ba30_4f2d


title: nasal_epithelial_cell, cb14_4b6b


title: nasal_epithelial_cell, fdf7_4e1d


title: nasal_epithelial_cell, 7008_4df1


title: nasal_epithelial_cell, 5511_4a05


title: nasal_epithelial_cell, 191a_4f27


title: nasal_epithelial_cell, ba59_4e13


title: nasal_epithelial_cell, 6cfa_47eb


title: nasal_epithelial_cell, ec17_45cd


title: nasal_epithelial_cell, ba3c_4e7d


title: nasal_epithelial_cell, a7e0_4edc


title: nasal_epithelial_cell, 0953_495f


title: nasal_epithelial_cell, 1c5a_42b7


title: nasal_epithelial_cell, ce9d_48cb


title: nasal_epithelial_cell, 560c_45ae


title: nasal_epithelial_cell, a4c3_41bf


title: nasal_epithelial_cell, 320d_4d18


title: nasal_epithelial_cell, 9cde_4efb


title: nasal_epithelial_cell, 4558_40a1


title: nasal_epithelial_cell, f368_4079


title: nasal_epithelial_cell, 3035_4176


title: nasal_epithelial_cell, db1f_4966


title: nasal_epithelial_cell, a761_4cbb


title: nasal_epithelial_cell, 728e_4557


title: nasal_epithelial_cell, 440b_434e


title: nasal_epithelial_cell, 9b1e_4e04


title: nasal_epithelial_cell, ca96_4770


title: nasal_epithelial_cell, 683a_481b


title: nasal_epithelial_cell, 8630_442b


title: nasal_epithelial_cell, 2af2_4f74


title: nasal_epithelial_cell, 3f99_40fc


title: nasal_epithelial_cell, af1a_4fc0


title: nasal_epithelial_cell, 4aa5_446a


title: nasal_epithelial_cell, d1d6_4694


title: nasal_epithelial_cell, ecb5_42ad


title: nasal_epithelial_cell, 6b78_4e91


title: nasal_epithelial_cell, 151a_48e4


title: nasal_epithelial_cell, 17f2_49a2


title: nasal_epithelial_cell, 3b4c_4c38


title: nasal_epithelial_cell, b63c_45ae


title: nasal_epithelial_cell, 07bf_4890


title: nasal_epithelial_cell, 71a4_49f7


title: nasal_epithelial_cell, 2377_438e


title: nasal_epithelial_cell, 7dc8_4e58


title: nasal_epithelial_cell, 7b00_435d


title: nasal_epithelial_cell, c50c_469d


title: nasal_epithelial_cell, 2438_4a51


title: nasal_epithelial_cell, c35c_4b38


title: nasal_epithelial_cell, b181_4fa1


title: nasal_epithelial_cell, 5f62_4a4f


title: nasal_epithelial_cell, 1cd9_4233


title: nasal_epithelial_cell, cfdb_4d8e


title: nasal_epithelial_cell, a53e_446d


title: nasal_epithelial_cell, 0108_48a9


title: nasal_epithelial_cell, 4445_4c3f


title: nasal_epithelial_cell, 90ec_4507


title: nasal_epithelial_cell, 6f04_4513


title: nasal_epithelial_cell, 405d_45e4


title: nasal_epithelial_cell, 0613_4958


title: nasal_epithelial_cell, bb1f_45c7


title: nasal_epithelial_cell, ff12_43c1


title: nasal_epithelial_cell, 41c1_4c6c


title: nasal_epithelial_cell, 6eae_4bb6


title: nasal_epithelial_cell, e788_4420


title: nasal_epithelial_cell, 3070_4a2e


title: nasal_epithelial_cell, 39a2_4fa7


title: nasal_epithelial_cell, f60d_46d7


title: nasal_epithelial_cell, 00a0_4d9e


title: nasal_epithelial_cell, 446c_43a9


title: nasal_epithelial_cell, fa3c_4775


title: nasal_epithelial_cell, ccbc_438a


title: nasal_epithelial_cell, 0935_4a72


title: nasal_epithelial_cell, a66b_4478


title: nasal_epithelial_cell, 857d_47f0


title: nasal_epithelial_cell, 5e0e_4d25


title: nasal_epithelial_cell, 56f6_4755


title: nasal_epithelial_cell, 5f1c_4a2b


title: nasal_epithelial_cell, 8789_42ab


title: nasal_epithelial_cell, d597_4365


title: nasal_epithelial_cell, daed_4207


title: nasal_epithelial_cell, fdfa_4400


title: nasal_epithelial_cell, e580_4af5


title: nasal_epithelial_cell, 35b6_43b6


title: nasal_epithelial_cell, eaf9_434a


title: nasal_epithelial_cell, f491_4a20


title: nasal_epithelial_cell, 46a8_4999


title: nasal_epithelial_cell, f090_45b5


title: nasal_epithelial_cell, f9a6_4519


title: nasal_epithelial_cell, f5ca_4743


title: nasal_epithelial_cell, 6e1e_41da


title: nasal_epithelial_cell, 957b_4a81


title: nasal_epithelial_cell, 5d51_4893


title: nasal_epithelial_cell, b8fe_4cf9


title: nasal_epithelial_cell, b0dc_4562


title: nasal_epithelial_cell, 0bae_4249


title: nasal_epithelial_cell, 3ba4_4b60


title: nasal_epithelial_cell, 5349_46fc


title: nasal_epithelial_cell, 3b1a_47d9


title: nasal_epithelial_cell, bea8_4a92


title: nasal_epithelial_cell, 427a_4a32


title: nasal_epithelial_cell, aa5a_4b8b


title: nasal_epithelial_cell, f536_458e


title: nasal_epithelial_cell, 8bd0_4bee


title: nasal_epithelial_cell, d38d_4047


title: nasal_epithelial_cell, c1ea_44f3


title: nasal_epithelial_cell, f142_42c4


title: nasal_epithelial_cell, 0848_4e53


title: nasal_epithelial_cell, 5260_47ad


title: nasal_epithelial_cell, d112_4a28


title: nasal_epithelial_cell, 4483_465d


title: nasal_epithelial_cell, 2e7c_4eb6


title: nasal_epithelial_cell, 8aff_46a6


title: nasal_epithelial_cell, ebba_4134


title: nasal_epithelial_cell, 4b90_43a1


title: nasal_epithelial_cell, 1a52_4c1f


title: nasal_epithelial_cell, 8327_4e30


title: nasal_epithelial_cell, de7b_417d


title: nasal_epithelial_cell, 5876_4bd6


title: nasal_epithelial_cell, 9bad_41f2


title: nasal_epithelial_cell, b844_44f0


title: nasal_epithelial_cell, 8b04_4d1b


title: nasal_epithelial_cell, b0c0_4808


title: nasal_epithelial_cell, 8ba5_4876


title: nasal_epithelial_cell, e242_4506


title: nasal_epithelial_cell, 3263_4372


title: nasal_epithelial_cell, 01fd_4b75


title: nasal_epithelial_cell, 83cb_478f


title: nasal_epithelial_cell, 20df_4e99


title: nasal_epithelial_cell, ebbe_4c60


title: nasal_epithelial_cell, 80e7_4747


title: nasal_epithelial_cell, 4a4e_48ff


title: nasal_epithelial_cell, 726a_4fda


title: nasal_epithelial_cell, cabb_4beb


title: nasal_epithelial_cell, 1e87_4d28


title: nasal_epithelial_cell, 2c24_4642


title: nasal_epithelial_cell, 1a58_42df


title: nasal_epithelial_cell, 0955_465a


title: nasal_epithelial_cell, 2107_4b5b


title: nasal_epithelial_cell, 62b8_4455


title: nasal_epithelial_cell, f88a_466a


title: nasal_epithelial_cell, 300d_4407


title: nasal_epithelial_cell, d659_4c43


title: nasal_epithelial_cell, b1df_40c8


title: nasal_epithelial_cell, 931f_471f


title: nasal_epithelial_cell, 5315_468e


title: nasal_epithelial_cell, 7bed_40f3


title: nasal_epithelial_cell, 1dfb_4de3


title: nasal_epithelial_cell, 8a01_4780


title: nasal_epithelial_cell, cdad_4a26


title: nasal_epithelial_cell, 57c7_4349


title: nasal_epithelial_cell, 5df4_4413


title: nasal_epithelial_cell, aeba_4a49


title: nasal_epithelial_cell, 1da9_41ad


title: nasal_epithelial_cell, 28f8_4130


title: nasal_epithelial_cell, 1b23_44ba


title: nasal_epithelial_cell, 1ea6_4250


title: nasal_epithelial_cell, df7b_40e5


title: nasal_epithelial_cell, 11f5_4b20


title: nasal_epithelial_cell, a3ce_4f1d


title: nasal_epithelial_cell, 37df_47b2


title: nasal_epithelial_cell, b254_4c91


title: nasal_epithelial_cell, d5ae_4497


title: HIF response activator screen FACS day8 GFP low 1% oxygen

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description: exp2 (activator screen)

data_processing:
Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with Cutadapt
Read counts were generated using HISAT2
Enriched sgRNAs were detected with MAGeCK
Assembly: custom human sgRNA library against known DUBs
Supplementary files format and content: Text files with a count for each individual sgRNA
Library strategy: CRISPR-Cas9 screens seq

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM and supplemented with 10% FCS

extract_protocol:
Gentra Puregene Core DNA extraction kit
Viral inserts are amplified and index sequences added by PCR

treatment_protocol: Hypoxic cell culture was performed in a Whitley H35 Hypoxystation at 37 °C, 5% CO2, 1 % O2and 94% N2.

value: HeLa

value: HIF-ODD GFP reporter

value: FACS for GFP low 1% oxygen


title: HIF response activator screen no FACS day8

description: exp2 (activator screen)

value: No FACS


title: nasal_epithelial_cell, 615a_4ba9


title: nasal_epithelial_cell, 03a0_49cb


title: nasal_epithelial_cell, 1dbd_4dec


title: HIF response suppressor screen no FACS day8 21% oxygen

description: exp1 (suppressor screen)

value: No FACS 21% oxygen


title: A549 cells, secondary, REP2

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: Gene expression data for secondary infection

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression signal was normalized using the Robust Multichip Average (RMA) method, from the affy R package. Control and lowly express probes were filtered out and the replicate effect was removed using the ComBat approach implemented in the sva R package.

source_name: secondary

label_protocol: The Affymetrix Human Gene array 2.1 microarrays was performed by Eurofins Genomics (France).

growth_protocol: The human alveolar epithelial cell line A549 (ATCC CCL-185) were cultured in F-12K culture medium (Gibco™ 21127030) supplemented with 10% fetal calf serum (FCS) and 1% L-glutamine and incubated at 37 °C in a humidified atmosphere with 5% CO2. Bacteria (pneumococcus) were diluted in serum-low cell culture medium (0,25% FCS) to get a multiplicity of infection of 20:1 (MOI 20). After 3h of  infection (primary), cells were washed twice with PBS to remove the unattached bacteria, and then either collected for analysis, or cultured in medium with penicillin-streptomycin (10 microg /ml) and gentamicin (200 microg /ml) during 4 days for later time point.  At 7 days post infection (PI), the cells were no infected or a second infection (secondary) is performed during 3 h.

extract_protocol: RNA was extracted from cells using RNeasy Mini Kit (Qiagen, 74104) and protocol followed according to manufacturers’ instructions. Chloroform extraction/Na-Acetate 3M (pH 5.5), isopropanol precipitated and washed 3 times in 70% ethanol prior to being suspended in molecular grade water. Extracted RNA quality was assessed and quantified with RNA 6000 Nano kit (Agilent, 5067-1511) using 2100 Bioanalyzer instrument (Agilent).

value: lung carcinoma epithelial cells

tag: infection

value: secondary infection


title: HIF response suppressor screen FACS day8 GFP high 21% oxygen

description: exp1 (suppressor screen)

value: FACS for GFP high 21% oxygen


title: nasal_epithelial_cell, b6fb_48d6

value: female


title: nasal_epithelial_cell, fc3f_4791

value: male


title: A549 cells, primary, REP2

description: Gene expression data for primary infection

source_name: primary

value: primary infection


title: A549 cells, primary, REP3


title: A549 cells, secondary, REP1


title: A549 cells, PI, REP3

description: Gene expression data for PI

source_name: PI

value: PI


title: A549 cells, PI, REP1

description: Gene expression data for PI


title: A549 cells, UI, REP3

description: Gene expression data for UI

source_name: UI

value: UI


title: A549 cells, PI, REP2

description: Gene expression data for PI


title: A549 cells, secondary, REP3


title: nasal_epithelial_cell, 3c6d_45ca


title: A549 cells, UI, REP1

description: Gene expression data for UI


title: A549 cells, UI, REP2

description: Gene expression data for UI


title: A549 cells, primary, REP1


title: nasal_epithelial_cell, 02fe_452f


title: nasal_epithelial_cell, 1136_495c


title: Embryo, 24h_post_KO_crispr_guide_capture, replicate 3

city: London

first: Ashley

middle: RG

last: Libby

address: 1 Midland Rd

institute: The Francis Crick Insitute

description: 10x Genomics Chromium Single-Cell 3′ mRNA V3.1 and 3’ Feature Barcode Kit

data_processing:
All GEX datasets were processes using Cell Ranger (v4.0.0, 10X Genomics), where FASTQ files were generated via the cell ranger count pipeline and CRISPR barcodes were analysed via the CRISPR guide capture analysis pipeline. FASTQ were aligned to the white leghorn GRCg7w reference genome with the addition of the Citrine transgene.
From the Cell Ranger pipelines, the Seurat package (version 4.3.2)(Butler et al., 2018; Satija et al., 2015) was used in R (version 4.3.2) to analyse the resultant FASTQ files. For the Rito et al. dataset, removal of outliers for quality control included thresholds based on the numbers of genes/features (nCount_RNA > 2500, nFeature_RNA >300 & nFeature_RNA < 3500, mitochondrial gene percentage < 10% & mitochondrial gene percentage > 0.5%). Principal component analysis was used to identify the most variable genes and the top 30 principal components used to define a 16 cluster UMAP via the functions FindNeighbors, FindClusters, RunUMAP and DimPlot with a resolution boundary of 0.9.
Assembly: Gallus gallus GRCg7w
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx (Files were generated using the Cell Ranger.)
Supplementary files format and content: json (each json file includes the detected protospacer or CRISPR guide per sequenced cell  in the parallel replicate sample. Files were generated using the Cell Ranger count and CRISPR guide capture analysis pipeline.)

organism: Gallus gallus

source_name: trunk of embryo

extract_protocol:
Embryos were isolated and dissociated to a single cell suspension by incubating in 200ul of dissociation solution consisting of Accutase (Stemcell Technologies, 07922) with 3U/mg Papain (Sigma-Aldrich, 10108014001) and 1mg/mL of Collagenase 4 (Gibco, 17104019) for 20 minutes.  Additionally, cells were briefly mechanically dissociated after the first 10 minutes incubation in dissociated solution with a P1000 pipet. Subsequently, 200μL of DPBS was added, suspension filtered through a 40μm Flowmi cell strainer (Sigma-Aldrich, 136800040). Cells were spun for 4 minutes at 400g and resuspended in PBS+ 0.5% BSA (Sigma-Aldrich, A2153) and kept on ice for subsequent analysis. Single cell suspensions were counted post FACS and viability of >90% was ensured.
A single cell suspension was loaded onto a Chromium Chip G and run on the 10x Chromium Controller (PN-1000120). The cells were then processed via the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268) protocol and the 3’ Feature Barcode Kit, 16 rxns (PN-1000262). cDNA synthesis, library construction, and feature PCR amplification were performed via manufacturer’s protocol. Samples were then sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs aiming for 50,000 reads per cell (between 30k-50k depending on sample).

value: trunk of embryo

value: pooled CRISPR screen


title: Embryo, 24h_post_KO_gene_expression, replicate 4


title: nasal_epithelial_cell, 3d49_4214


title: Embryo, 24h_post_KO_crispr_guide_capture, replicate 4


title: Embryo, 24h_post_KO_crispr_guide_capture, replicate 2


title: Embryo, 24h_post_KO_gene_expression, replicate 3


title: nasal_epithelial_cell, f3bc_4614

value: hispanic


title: Embryo, 24h_post_KO_gene_expression, replicate 2


title: Embryo, 24h_post_KO_crispr_guide_capture, replicate 1


title: nasal_epithelial_cell, 677f_4f07


title: nasal_epithelial_cell, fd68_4250

value: multiple


title: nasal_epithelial_cell, 51c2_4fe8


title: Embryo, 24h_post_KO_gene_expression, replicate 1


title: nasal_epithelial_cell, 7ee2_452a


title: nasal_epithelial_cell, e1f4_491f